The version you are using is buggy in IE9 (Haven't tested other versions of IE, nor other versions of Prototype except the ones below). I advise you to update Prototype. Test this in the console (F12 tools):
Version 1.7:
(new Element('div', {className: 'buggy'})).outerHTML
returns "<div class="buggy"></div>"
(new Element('div', {class: 'buggy'})).outerHTML
returns "<div class="buggy"></div>"
Version 1.6.0.3:
(new Element('div', {className: 'buggy'})).outerHTML
returns "<div className="buggy"></div>"
(new Element('div', {class: 'buggy'})).outerHTML
returns "<div className="buggy"></div>"
(Sorry for the late response, I just had to debug this in IE9)